scholarly journals Structure-based inhibitors targeting the alpha-helical domain of the Spiroplasma melliferum histone-like HU protein

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yuliya K. Agapova ◽  
Dmitry A. Altukhov ◽  
Vladimir I. Timofeev ◽  
Victor S. Stroylov ◽  
Vitaly S. Mityanov ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein A ◽  
Site Directed Mutagenesis ◽  
Mycoplasma Species ◽  
Helical Domain ◽  
Hu Protein ◽  
Dimerization Interface ◽  
Associated Proteins ◽  
Pharmacological Potential ◽  
Spiroplasma Melliferum

Abstract Here we report bisphenol derivatives of fluorene (BDFs) as a new type of chemical probes targeting a histone-like HU protein, a global regulator of bacterial nucleoids, via its dimerization interface perturbation. BDFs were identified by virtual screening and molecular docking that targeted the core of DNA-binding β-saddle-like domain of the HU protein from Spiroplasma melliferum. However, NMR spectroscopy, complemented with molecular dynamics and site-directed mutagenesis, indicated that the actual site of the inhibitors’ intervention consists of residues from the α-helical domain of one monomer and the side portion of the DNA-binding domain of another monomer. BDFs inhibited DNA-binding properties of HU proteins from mycoplasmas S. melliferum, Mycoplasma gallicepticum and Escherichia coli with half-maximum inhibitory concentrations in the range between 5 and 10 µM. In addition, BDFs demonstrated antimicrobial activity against mycoplasma species, but not against E. coli, which is consistent with the compensatory role of other nucleoid-associated proteins in the higher bacteria. Further evaluation of antimicrobial effects of BDFs against various bacteria and viruses will reveal their pharmacological potential, and the allosteric inhibition mode reported here, which avoids direct competition for the binding site with DNA, should be considered in the development of small molecule inhibitors of nucleoid-associated proteins as well as other types of DNA-binding multimeric proteins.

scholarly journals Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the histone-like HU protein fromSpiroplasma melliferumKC3

2015 ◽  
Vol 71 (1) ◽  
pp. 24-27 ◽  
Author(s):  
Konstantin Boyko ◽  
Marina Gorbacheva ◽  
Tatiana Rakitina ◽  
Dmitry Korzhenevskiy ◽  
Anna Vanyushkina ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
Molecular Replacement ◽  
Dna Compaction ◽  
Hu Protein ◽  
Replacement Method ◽  
Hu Proteins ◽  
Diffusion Technique ◽  
Associated Proteins ◽  
Molecular Replacement Method ◽  
Spiroplasma Melliferum

HU proteins belong to the nucleoid-associated proteins (NAPs) that are involved in vital processes such as DNA compaction and reparation, gene transcriptionetc.No data are available on the structures of HU proteins from mycoplasmas. To this end, the HU protein from the parasitic mycoplasmaSpiroplasma melliferumKC3 was cloned, overexpressed inEscherichia coliand purified to homogeneity. Prismatic crystals of the protein were obtained by the vapour-diffusion technique at 4°C. The crystals diffracted to 1.36 Å resolution (the best resolution ever obtained for a HU protein). The diffraction data were indexed in space groupC2 and the structure of the protein was solved by the molecular-replacement method with one monomer per asymmetric unit.

scholarly journals Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12

2011 ◽  
Vol 40 (8) ◽  
pp. 3524-3537 ◽  
Author(s):  
Ana I. Prieto ◽  
Christina Kahramanoglou ◽  
Ruhi M. Ali ◽  
Gillian M. Fraser ◽  
Aswin S. N. Seshasayee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gene Regulation ◽  
Dna Binding ◽  
Genomic Analysis ◽  
Escherichia Coli K12 ◽  
Associated Proteins

scholarly journals Cross-Talk between PPARs and the Partners of RXR: A Molecular Perspective

PPAR Research ◽  
2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Lap Shu Alan Chan ◽  
Richard A. Wells
Keyword(s):  
Dna Binding ◽  
Nuclear Receptors ◽  
Cross Talk ◽  
Molecular Level ◽  
Signaling Networks ◽  
Future Studies ◽  
Functional Roles ◽  
Dimerization Interface ◽  
Experimental Approaches ◽  
Nuclear Receptor Subfamily

The PPARs are integral parts of the RXR-dependent signaling networks. Many other nuclear receptor subfamily 1 members also require RXR as their obligatory heterodimerization partner and they are often co-expressed in any given tissue. Therefore, the PPARs often complete with other RXR-dependent nuclear receptors and this competition has important biological implications. Thorough understanding of this cross-talk at the molecular level is crucial to determine the detailed functional roles of the PPARs. At the level of DNA binding, most RXR heterodimers bind selectively to the well-known “DR1 to 5” DNA response elements. As a result, many heterodimers share the same DR element and must complete with each other for DNA binding. At the level of heterodimerization, the partners of RXR share the same RXR dimerization interface. As a result, individual nuclear receptors must complete with each other for RXR to form functional heterodimers. Cross-talk through DNA binding and RXR heterodimerization present challenges to the study of these nuclear receptors that cannot be adequately addressed by current experimental approaches. Novel tools, such as engineered nuclear receptors with altered dimerization properties, are currently being developed. These tools will enable future studies to dissect specific RXR heterodimers and their signaling pathways.

Genetic Analysis of Yeast RPA1 Reveals Its Multiple Functions in DNA Metabolism

Genetics ◽  
1998 ◽  
Vol 148 (3) ◽  
pp. 989-1005 ◽  
Author(s):  
Keiko Umezu ◽  
Neal Sugawara ◽  
Clark Chen ◽  
James E Haber ◽  
Richard D Kolodner
Keyword(s):  
Dna Replication ◽  
Dna Binding ◽  
Protein A ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Physical Analysis ◽  
Single Stranded Dna ◽  
Temperature Sensitive Mutants

Abstract Replication protein A (RPA) is a single-stranded DNA-binding protein identified as an essential factor for SV40 DNA replication in vitro. To understand the in vivo functions of RPA, we mutagenized the Saccharomyces cerevisiae RFA1 gene and identified 19 ultraviolet light (UV) irradiation- and methyl methane sulfonate (MMS)-sensitive mutants and 5 temperature-sensitive mutants. The UV- and MMS-sensitive mutants showed up to 104 to 105 times increased sensitivity to these agents. Some of the UV- and MMS-sensitive mutants were killed by an HO-induced double-strand break at MAT. Physical analysis of recombination in one UV- and MMS-sensitive rfa1 mutant demonstrated that it was defective for mating type switching and single-strand annealing recombination. Two temperature-sensitive mutants were characterized in detail, and at the restrictive temperature were found to have an arrest phenotype and DNA content indicative of incomplete DNA replication. DNA sequence analysis indicated that most of the mutations altered amino acids that were conserved between yeast, human, and Xenopus RPA1. Taken together, we conclude that RPA1 has multiple roles in vivo and functions in DNA replication, repair, and recombination, like the single-stranded DNA-binding proteins of bacteria and phages.

Suppression of albumin enhancer activity by H-ras and AP-1 in hepatocyte cell lines

1994 ◽  
Vol 14 (3) ◽  
pp. 1531-1543
Author(s):  
J Hu ◽  
H C Isom
Keyword(s):  
Dna Binding ◽  
Cell Line ◽  
Cell Lines ◽  
Binding Sites ◽  
Simian Virus 40 ◽  
Site Directed Mutagenesis ◽  
Ras Signaling ◽  
Enhancer Activity ◽  
Hepatocyte Cell Line ◽  
Transformed Cell Lines

We demonstrated, using a transient transfection assay, that the albumin enhancer increased the expression of the albumin promoter in a highly differentiated, simian virus 40 (SV40)-immortalized hepatocyte cell line, CWSV1, but was not functional in two ras-transformed cell lines (NR3 and NR4) derived from CWSV1 by stable transfection with the T24ras oncogene. A transient cotransfection assay showed that T24ras and normal c-Ha-ras were each able to inhibit the activity of the albumin enhancer in an immortal hepatocyte cell line. DNase I footprinting and gel mobility shift assays demonstrated that the DNA binding activities specific to the albumin enhancer were not decreased in the ras-transformed cells. ras also did not diminish the expression of HNF1 alpha, C/EBP alpha, HNF3 alpha, HNF3 beta, or HNF3 gamma but did significantly increase AP-1 binding activity. Three AP-1 binding sites were identified within the albumin enhancer, and DNA binding activities specific to these AP-1 sites were induced in the ras-transformed hepatocytes. Subsequent functional assays showed that overexpression of c-jun and c-fos inhibited the activity of the albumin enhancer. Site-directed mutagenesis of the AP-1 binding sites in the albumin enhancer partially abrogated the suppressing effect of ras and c-jun/c-fos on the enhancer. These functional studies therefore supported the results of the structural studies with AP-1. We conclude that the activity of the albumin enhancer is subject to regulation by ras signaling pathways and that the effect of ras on the albumin enhancer activity may be mediated by AP-1.

Functionally distinct isoforms of the CRE-BP DNA-binding protein mediate activity of a T-cell-specific enhancer

1992 ◽  
Vol 12 (2) ◽  
pp. 747-757
Author(s):  
K Georgopoulos ◽  
B A Morgan ◽  
D D Moore
Keyword(s):  
T Cell ◽  
Dna Binding ◽  
Cyclic Amp ◽  
Protein A ◽  
Cell Receptor ◽  
Protein Isoforms ◽  
Cdna Clones ◽  
C Terminus ◽  
Transcription Regulators ◽  
Cyclic Amp Response Element

Expression of the CD3 delta gene of the T-cell receptor (TCR) complex is regulated by a T-cell-specific enhancer. A highly conserved 40-bp motif (element delta A) within the CD3 delta enhancer is responsible for mediating its activity and specificity. Element delta A exhibits sequence similarities to the cyclic AMP response element (CRE) but does not respond to changes in the level of cyclic AMP. Using the delta A element as a probe, we have isolated three cDNA clones encoding three distinct protein isoforms, products of differential splicing and alternate promoter usage of the CRE-BP gene. These isoforms share the DNA binding and dimerization domains at the C terminus of the protein but differ at their N termini. In transfection assays, their activities as transcription regulators differ: CRE-BP2 is a potent activator, CRE-BP3 is a weak activator, and CRE-BP1 is transcriptionally inert. Mutations in the basic region of the CRE-BP1 protein which abrogate its ability to bind DNA render this protein a dominant repressor of the delta A enhancer. Antibodies to the CRE-BP protein interact specifically with the ubiquitous and predominantly T-cell-restricted nuclear complexes that bind to the delta A element and suggest the presence of this protein in homo- and heterodimeric complexes. Since the delta A motif is also present in the enhancer and promoter of the TCR alpha and beta genes, the CRE-BP isoforms may mediate expression of other members of the CD3/TCR complex during T-cell development.

Sign in / Sign up

Export Citation Format

Share Document